rs2250072

Positions:

• chr15-48092710-A-G
• chr15-48092710-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.339 in 152,098 control chromosomes in the GnomAD database, including 17,227 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (17227 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51380 AN: 151980 Hom.: 17164 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.290

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.339 AC: 51508 AN: 152098 Hom.: 17227 Cov.: 32 AF XY: 0.338 AC XY: 25108 AN XY: 74378

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.0833

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.0414

Gnomad4 NFE AF: 0.0803

Gnomad4 OTH AF: 0.297

Alfa AF: 0.131 Hom.: 4741

Bravo AF: 0.389

Asia WGS AF: 0.664 AC: 2307 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.57
DANN	Benign	0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2250072; hg19: chr15-48384907;